Package picard.analysis.artifacts
Class SequencingArtifactMetrics.PreAdapterSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
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- Enclosing class:
- SequencingArtifactMetrics
public static class SequencingArtifactMetrics.PreAdapterSummaryMetrics extends htsjdk.samtools.metrics.MetricBase
Summary analysis of a single pre-adapter artifact. These artifacts occur on the original template strand, before the addition of adapters, so they correlate with read number / orientation in a specific way. For example, the well-known "Oxo-G" artifact occurs when a G on the template strand is oxidized, giving it an affinity for binding to A rather than the usual C. Thus PCR will introduce apparent G>T substitutions in read 1 and C>A in read 2. In the resulting alignments, a given G>T or C>A observation could either be: 1. a true mutation 2. an OxoG artifact 3. some other kind of artifact On average, we assume that 1 and 3 will not display this read number / orientation bias, so their contributions will cancel out in the calculation.
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Field Summary
Fields Modifier and Type Field Description char
ALT_BASE
The (upper-case) alternative base that is called as a result of DNA damage.String
ARTIFACT_NAME
A "nickname" of this artifact, if it is a known error mode.String
LIBRARY
The name of the library being assayed.char
REF_BASE
The (upper-case) original base on the reference strand.String
SAMPLE_ALIAS
The name of the sample being assayed.double
TOTAL_QSCORE
The total Phred-scaled Q-score for this artifact.String
WORST_CXT
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.double
WORST_CXT_QSCORE
The Q-score for the worst context.String
WORST_POST_CXT
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.double
WORST_POST_CXT_QSCORE
The Q-score for the worst post-context.String
WORST_PRE_CXT
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.double
WORST_PRE_CXT_QSCORE
The Q-score for the worst pre-context.
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Constructor Summary
Constructors Constructor Description PreAdapterSummaryMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
inferArtifactName()
Label the artifacts corresponding to known error modes.
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Field Detail
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SAMPLE_ALIAS
public String SAMPLE_ALIAS
The name of the sample being assayed.
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LIBRARY
public String LIBRARY
The name of the library being assayed.
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REF_BASE
public char REF_BASE
The (upper-case) original base on the reference strand.
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ALT_BASE
public char ALT_BASE
The (upper-case) alternative base that is called as a result of DNA damage.
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TOTAL_QSCORE
public double TOTAL_QSCORE
The total Phred-scaled Q-score for this artifact. A lower Q-score means a higher probability that a REF_BASE:ALT_BASE observation randomly picked from the data will be due to this artifact, rather than a true variant.
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WORST_CXT
public String WORST_CXT
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
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WORST_CXT_QSCORE
public double WORST_CXT_QSCORE
The Q-score for the worst context.
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WORST_PRE_CXT
public String WORST_PRE_CXT
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
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WORST_PRE_CXT_QSCORE
public double WORST_PRE_CXT_QSCORE
The Q-score for the worst pre-context.
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WORST_POST_CXT
public String WORST_POST_CXT
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
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WORST_POST_CXT_QSCORE
public double WORST_POST_CXT_QSCORE
The Q-score for the worst post-context.
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ARTIFACT_NAME
public String ARTIFACT_NAME
A "nickname" of this artifact, if it is a known error mode.
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